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Bacterial whole genome sequencing

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https://www.readbyqxmd.com/read/28096484/evolutionary-dynamics-of-pandemic-methicillin-sensitive-staphylococcus-aureus-st398-and-its-international-spread-via-routes-of-human-migration
#1
Anne-Catrin Uhlemann, Paul R McAdam, Sean B Sullivan, Justin R Knox, Hossein Khiabanian, Raul Rabadan, Peter R Davies, J Ross Fitzgerald, Franklin D Lowy
: Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for the majority of S. aureus infections globally, and yet surprisingly little is known about its clonal evolution. We applied comparative whole-genome sequencing (WGS) analyses to epidemiologically and geographically diverse ST398-MSSA, a pandemic lineage affecting both humans and livestock. Bayesian phylogenetic analysis predicted divergence of human-associated ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and veterinarians differed substantially from those in New York City (NYC)...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28095770/the-unique-genomic-landscape-surrounding-the-epsps-gene-in-glyphosate-resistant-amaranthus-palmeri-a-repetitive-path-to-resistance
#2
William T Molin, Alice A Wright, Amy Lawton-Rauh, Christopher A Saski
BACKGROUND: The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment...
January 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28091882/identification-of-some-main-streptococcus-iniae-associated-proteins-relationship
#3
Fatima El Aamri, José Ángel Guillén, Daniel Padilla, Félix Acosta, Fernando Real
The surface-associated proteins play a key role in bacterial physiology and pathogenesis, and are the major targets in the development of new vaccines. These proteins contribute to the adaptation of bacteria to different hosts and environments. To study differences at the genomic level, we first sequenced the whole genome of Streptococcus iniae from fish (IUSA-1 strain) and compared it to Streptococcus iniae from human (9117 strain), revealing a high similitude between both strains. To gain further insights into host- and environment-specific differences, we then studied proteins in silico and by High Performance Liquid Chromatography...
January 14, 2017: Veterinary Research Communications
https://www.readbyqxmd.com/read/28087649/identification-of-unique-essential-proteins-from-a-m-tuberculosis-f15-lam4-kzn-phage-secretome-library
#4
Thamsanqa Emmanuel Chiliza, Manormoney Pillay, Balakrishna Pillay
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis disease (TB), the leading cause of death from bacterial infection worldwide. Although treatable, the resurgence of multi- and extensively-drug resistance TB is a major setback for the fight against TB globally. Consequently, there is an urgent need for new Mtb derived biomarkers for use in the design of new drugs and rapid point-of-care diagnostic or prognostic tools for management of TB transmission. Therefore, the present study aimed to identify unique Mtb secreted proteins from the extensively drug resistant Mtb F15/LAM4/KZN phage secretome library...
January 12, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28081123/yersinia-enterocolitica-a-neglected-cause-of-human-enteric-infections-in-c%C3%A3-te-d-ivoire
#5
Daniel Saraka, Cyril Savin, Stephane Kouassi, Bakary Cissé, Eugène Koffi, Nicolas Cabanel, Sylvie Brémont, Hortense Faye-Kette, Mireille Dosso, Elisabeth Carniel
BACKGROUND: Enteropathogenic Yersinia circulate in the pig reservoir and are the third bacterial cause of human gastrointestinal infections in Europe. In West Africa, reports of human yersiniosis are rare. This study was conducted to determine whether pathogenic Yersinia are circulating in pig farms and are responsible for human infections in the Abidjan District. METHODOLOGY/PRINCIPAL FINDINGS: From June 2012 to December 2013, pig feces were collected monthly in 41 swine farms of the Abidjan district...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28074024/whole-genome-sequencing-of-invasion-resistant-cells-identifies-laminin-%C3%AE-2-as-a-host-factor-for-bacterial-invasion
#6
Xander M van Wijk, Simon Döhrmann, Björn M Hallström, Shangzhong Li, Bjørn G Voldborg, Brandon X Meng, Karen K McKee, Toin H van Kuppevelt, Peter D Yurchenco, Bernhard O Palsson, Nathan E Lewis, Victor Nizet, Jeffrey D Esko
: To understand the role of glycosaminoglycans in bacterial cellular invasion, xylosyltransferase-deficient mutants of Chinese hamster ovary (CHO) cells were created using clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated gene 9 (CRISPR-cas9) gene targeting. When these mutants were compared to the pgsA745 cell line, a CHO xylosyltransferase mutant generated previously using chemical mutagenesis, an unexpected result was obtained. Bacterial invasion of pgsA745 cells by group B Streptococcus (GBS), group A Streptococcus, and Staphylococcus aureus was markedly reduced compared to the invasion of wild-type cells, but newly generated CRISPR-cas9 mutants were only resistant to GBS...
January 10, 2017: MBio
https://www.readbyqxmd.com/read/28072891/molecular-epidemiology-and-resistome-analysis-of-multidrug-resistant-st11-klebsiella-pneumoniae-strain-containing-multiple-copies-of-extended-spectrum-%C3%AE-lactamase-genes-using-whole-genome-sequencing
#7
Roshan DSouza, Naina Adren Pinto, Insik Hwang, Hwang Younjee, YoungLag Cho, Hyunsoo Kim, Dongeun Yong, Jongrak Choi, Kyungwon Lee, Yunsop Chong
The aim of this work was to investigate the mechanism responsible for multidrug resistance in ST11 Klebsiella pneumoniae YMC 2013/7/B3993 containing multiple copies of ESBL genes using multiple parallel sequencing technology. In-depth analysis of the strain revealed multiple copies of ESBL genes, 2 copies of blaSHV-12 and 1 copy of blaCTX-M-15. Furthermore, 1 copy of blaOXA-9 and 3 copies of blaTEM-1 were found. The insertion of Tn1331 was detected, which consisted of blaOXA-9, blaTEM-1, aac(6')-lb-cr, and aadA1 genes...
January 10, 2017: New Microbiologica
https://www.readbyqxmd.com/read/28069632/a-few-sequence-polymorphisms-among-isolates-of-maize-bushy-stunt-phytoplasma-associate-with-organ-proliferation-symptoms-of-infected-maize-plants
#8
Zigmunds Orlovskis, Maria Cristina Canale, Mindia Haryono, João Roberto Spotti Lopes, Chih-Horng Kuo, Saskia A Hogenhout
BACKGROUND AND AIMS: Maize bushy stunt phytoplasma (MBSP) is a bacterial pathogen of maize (Zea mays L.) across Latin America. MBSP belongs to the 16SrI-B sub-group within the genus 'Candidatus Phytoplasma'. MBSP and its insect vector Dalbulus maidis (Hemiptera: Cicadellidae) are restricted to maize; both are thought to have coevolved with maize during its domestication from a teosinte-like ancestor. MBSP-infected maize plants show a diversity of symptoms. and it is likely that MBSP is under strong selection for increased virulence and insect transmission on maize hybrids that are widely grown in Brazil...
January 9, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28066711/metagenomic-analysis-of-microbial-community-of-a-parasitoid-wasp-megaphragma-amalphitanum
#9
A V Nedoluzhko, F S Sharko, S V Tsygankova, E S Boulygina, A S Sokolov, S M Rastorguev, V V Kadnikov, A V Mardanov, N V Ravin, A M Mazur, A A Polilov, N M Gruzdeva, E B Prokhortchouk, K G Skryabin
The vast majority of multicellular organisms coexist with bacterial symbionts that may play various roles during their life cycle. Parasitoid wasp Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae) belongs to the smallest known insects whose size is comparable with some bacteria. Using 16S rRNA gene sequencing and Whole Genome Sequencing (WGS), we described microbiota diversity for this arthropod and its potential impact on their lifecycle. Metagenomic sequences were deposited to SRA database which is available at NCBI with accession number SRX2363723 and SRX2363724...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28065170/multistate-outbreak-of-listeria-monocytogenes-infections-linked-to-whole-apples-used-in-commercially-produced-prepackaged-caramel-apples-united-states-2014-2015
#10
K M Angelo, A R Conrad, A Saupe, H Dragoo, N West, A Sorenson, A Barnes, M Doyle, J Beal, K A Jackson, S Stroika, C Tarr, Z Kucerova, S Lance, L H Gould, M Wise, B R Jackson
Whole apples have not been previously implicated in outbreaks of foodborne bacterial illness. We investigated a nationwide listeriosis outbreak associated with caramel apples. We defined an outbreak-associated case as an infection with one or both of two outbreak strains of Listeria monocytogenes highly related by whole-genome multilocus sequence typing (wgMLST) from 1 October 2014 to 1 February 2015. Single-interviewer open-ended interviews identified the source. Outbreak-associated cases were compared with non-outbreak-associated cases and traceback and environmental investigations were performed...
January 9, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28063330/endolysin-lyssa97-is-synergistic-with-carvacrol-in-controlling-staphylococcus-aureus-in-foods
#11
Yoonjee Chang, Hyunjin Yoon, Dong-Hyun Kang, Pahn-Shick Chang, Sangryeol Ryu
LysSA97 is an endolysin encoded by the bacteriophage SA97, the genome sequence of which has been recently revealed. LysSA97 has lytic activity against a variety of Staphylococcus strains that cause foodborne illness. In order to improve its potential as a biocontrol agent against Staphylococcus, various types of essential oil-derived active compounds were tested in combination with LysSA97; carvacrol exhibited significant synergistic effects when combined with LysSA97. The synergistic antimicrobial activity between endolysin and carvacrol in food products, including milk and beef, were investigated...
December 27, 2016: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28061753/treatment-efficacy-of-azithromycin-1%C3%A2-g-single-dose-versus-doxycycline-100%C3%A2-mg-twice-daily-for-7%C3%A2-days-for-the-treatment-of-rectal-chlamydia-among-men-who-have-sex-with-men-a-double-blind-randomised-controlled-trial-protocol
#12
Andrew Lau, Fabian Kong, Christopher K Fairley, Basil Donovan, Marcus Chen, Catriona Bradshaw, Mark Boyd, Janaki Amin, Peter Timms, Sepehr Tabrizi, David G Regan, David A Lewis, Anna McNulty, Jane S Hocking
BACKGROUND: Rectal infection with Chlamydia trachomatis is one of the most common bacterial sexually transmissible infections among men who have sex with men (MSM) with diagnosis rates continuing to rise. Current treatment guidelines recommend either azithromycin 1 g single dose or doxycycline 100 mg twice daily for 7 days. However, there are increasing concerns about treatment failure with azithromycin. We are conducting the first randomised controlled trial (RCT) to compare treatment efficacy of azithromycin versus doxycycline for the treatment of rectal chlamydia in MSM...
January 6, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28060810/whole-genome-sequence-analysis-of-salmonella-typhi-isolated-in-thailand-before-and-after-the-introduction-of-a-national-immunization-program
#13
Zoe A Dyson, Duy Pham Thanh, Ladaporn Bodhidatta, Carl Jeffries Mason, Apichai Srijan, Maia A Rabaa, Phat Voong Vinh, Tuyen Ha Thanh, Guy E Thwaites, Stephen Baker, Kathryn E Holt
Vaccines against Salmonella Typhi, the causative agent of typhoid fever, are commonly used by travellers, however, there are few examples of national immunization programs in endemic areas. There is therefore a paucity of data on the impact of typhoid immunization programs on localised populations of S. Typhi. Here we have used whole genome sequencing (WGS) to characterise 44 historical bacterial isolates collected before and after a national typhoid immunization program that was implemented in Thailand in 1977 in response to a large outbreak; the program was highly effective in reducing typhoid case numbers...
January 6, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28058637/efficient-screening-of-potential-cellulases-and-hemicellulases-produced-by-bosea-sp-fbzp-16-using-the-combination-of-enzyme-assays-and-genome-analysis
#14
Aicha Asma Houfani, Tomáš Větrovský, Petr Baldrian, Said Benallaoua
Identification of bacteria that produce carbohydrolytic enzymes is extremely important given the increased demand for these enzymes in many industries. Twenty lignocellulose-degrading bacterial isolates from Algerian compost and different soils were screened for their potential to produce different enzymes involved in biomass deconstruction. Based on 16S rRNA gene sequencing, the isolates belonged to Proteobacteria and Actinobacteria. Differences among species were reflected both as the presence/absence of enzymes or at the level of enzyme activity...
February 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28056767/bacterial-whole-genome-based-phylogeny-construction-of-a-new-benchmarking-dataset-and-assessment-of-some-existing-methods
#15
Johanne Ahrenfeldt, Carina Skaarup, Henrik Hasman, Anders Gorm Pedersen, Frank Møller Aarestrup, Ole Lund
BACKGROUND: Whole genome sequencing (WGS) is increasingly used in diagnostics and surveillance of infectious diseases. A major application for WGS is to use the data for identifying outbreak clusters, and there is therefore a need for methods that can accurately and efficiently infer phylogenies from sequencing reads. In the present study we describe a new dataset that we have created for the purpose of benchmarking such WGS-based methods for epidemiological data, and also present an analysis where we use the data to compare the performance of some current methods...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28053217/high-interlaboratory-reproducibility-and-accuracy-of-next-generation-sequencing-based-bacterial-genotyping-in-a-ring-trial
#16
Alexander Mellmann, Paal Skytt Andersen, Stefan Bletz, Alexander W Friedrich, Thomas A Kohl, Berit Lilje, Stefan Niemann, Karola Prior, John W Rossen, Dag Harmsen
Today, next-generation whole genome sequencing (WGS) technology is increasingly used to determine the genetic relationship of bacteria on a nearly whole genome level for infection control purposes and molecular surveillance. Here, we conducted a multicenter ring-trial comprising five laboratories to determine the reproducibility and accuracy of WGS-based typing.The participating laboratories sequenced 20 blind-coded Staphylococcus aureus DNA samples using the 250 bp paired-end chemistry for library preparation in a single sequencing run on an Illumina Miseq sequencer...
January 4, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28049430/spread-of-avian-pathogenic-escherichia-coli-st117-o78-h4-in-nordic-broiler-production
#17
Troels Ronco, Marc Stegger, Rikke Heidemann Olsen, Camilla Sekse, Anne Bang Nordstoga, Tarja Pohjanvirta, Berit Lilje, Ulrike Lyhs, Paal Skytt Andersen, Karl Pedersen
BACKGROUND: Escherichia coli infections known as colibacillosis constitute a considerable challenge to poultry farmers worldwide, in terms of decreased animal welfare and production economy. Colibacillosis is caused by avian pathogenic E. coli (APEC). APEC strains are extraintestinal pathogenic E. coli and have in general been characterized as being a genetically diverse population. In the Nordic countries, poultry farmers depend on import of Swedish broiler breeders which are part of a breeding pyramid...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28049122/generation-of-gene-edited-chrysanthemum-morifolium-using-multi-copy-transgenes-as-targets-and-markers
#18
Mitsuko Kishi-Kaboshi, Ryutaro Aida, Katsutomo Sasaki
The most widely used gene editing technology-the CRISPR/Cas9 system-employs a bacterial monomeric DNA endonuclease known as clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) and single-guide RNA (sgRNA) that directs Cas9 to a complementary target DNA. However, introducing mutations into higher polyploid plant species, especially for species without genome information, has been difficult. Chrysanthemum morifolium (chrysanthemum) is one of the most important ornamental plants, but it is a hexaploid with a large genome; moreover, it lacks whole genome information...
January 3, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28028547/recent-outbreaks-of-shigellosis-in-california-caused-by-two-distinct-populations-of-shigella-sonnei-with-either-increased-virulence-or-fluoroquinolone-resistance
#19
Varvara K Kozyreva, Guillaume Jospin, Alexander L Greninger, James P Watt, Jonathan A Eisen, Vishnu Chaturvedi
Shigella sonnei has caused unusually large outbreaks of shigellosis in California in 2014 and 2015. Preliminary data indicated the involvement of two distinct bacterial populations, one from San Diego and San Joaquin (SDi/SJo) and one from the San Francisco (SFr) Bay area. Whole-genome analysis and antibiotic susceptibility testing of 68 outbreak and archival isolates of S. sonnei were performed to investigate the microbiological factors related to these outbreaks. Both SDi/SJo and SFr populations, as well as almost all of the archival S...
November 2016: MSphere
https://www.readbyqxmd.com/read/28018370/whole-genome-sequences-of-xanthomonas-euvesicatoria-strains-clarify-taxonomy-and-reveal-a-stepwise-erosion-of-type-3-effectors
#20
Jeri D Barak, Taca Vancheva, Pierre Lefeuvre, Jeffrey B Jones, Sujan Timilsina, Gerald V Minsavage, Gary E Vallad, Ralf Koebnik
Multiple species of Xanthomonas cause bacterial spot of tomato (BST) and pepper. We sequenced five Xanthomonas euvesicatoria strains isolated from three continents (Africa, Asia, and South America) to provide a set of representative genomes with temporal and geographic diversity. LMG strains 667, 905, 909, and 933 were pathogenic on tomato and pepper, except LMG 918 elicited a hypersensitive reaction (HR) on tomato. Furthermore, LMG 667, 909, and 918 elicited a HR on Early Cal Wonder 30R containing Bs3. We examined pectolytic activity and starch hydrolysis, two tests which are useful in differentiating X...
2016: Frontiers in Plant Science
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